Having gone behind to Steven Pienaar's 39th-minute goal in the Premier League clash at Goodison Park, United appeared to be cruising to victory after Darren Fletcher, Nemanja Vidic and Dimitar Berbatov put them in control.
However, Tim Cahill powered home a header in the first minute of added time and Mikel Arteta's deflected strike levelled things up 60 seconds later to leave Ferguson fuming at a second defensive lapse in three games which cost them victory.
"It's amazing. We've thrown it away, like we did at the Fulham game (when Brede Hangeland hit an equaliser in the 89th minute)," he said.
"You have to have determination in situations like that.
"Today we were so wasteful with our chances. We could have scored five or six in the second half with great opportunities and that has come to haunt us.
"But saying that, to lose two goals in injury time is unthinkable.
"We had it under control and the game is finished - even when they scored a second. It is a terrible end for us."
Despite finding themselves under pressure for most of the first half, United were never overwhelmed by their hosts and once they equalised just before the break there appeared to be only one winner.
Ferguson was left to rue a number of missed chances which would have put the game beyond the Toffees' reach before their dramatic late comeback.
"We have thrown the points away and hopefully at the end of the season we don't sit back and regret it," he added.
"We had some great opportunities in the first half and I think most of the time we were the team who threatened most in terms of playing football.
"Vidic's goal was a good time to score but going 3-1 up you think you are in a comfortable position but football comes back to bite you.
"It has happened before and we have done it ourselves."
Everton manager David Moyes was disappointed his side had not capitalised on their early dominance to establish more of a platform before United worked their way back into the game.
Prior to this match the Toffees had scored just once in three matches and it appeared that bluntness in front of goal was to be their downfall once again until the late intervention of Cahill and Arteta.
"I thought our play in the first half merited more than what we had at half-time but that is how it goes," said the Scot.
"We expect that character but we stuck at it against a top team. But to be fair I, like probably most, thought that was it at 3-1 down.
"But at that time I didn't think we had played terribly badly I just through Manchester United took their chances when they got them."
Despite snatching a draw, Moyes ran on to the pitch at full-time to remonstrate with referee Martin Atkinson after he blew the final whistle with Everton on the attack.
"The two goals were scored after 90 minutes and they'd put up three minutes of extra time," he added.
"He didn't get his time right because there was more time to add on for the goals and he played three minutes 30 seconds.
"They had the corner kick and we had a great counter-attack and he blew up with the ball 25 yards from their goal.
"It is a spectator sport with people coming to watch the game and not for him to be the main man and the one who wants to be seen making the decisions.
"That was a terrible decision in my book."